(written from a Production point of view)
The USS Nile was a Danube-class runabout mentioned in the first draft script of DS9: "Shadows and Symbols" (dated 6 July 1998). The Nile was the ship that Benjamin, Jake, and Joseph Sisko, along with Ezri Dax, used to travel to Tyree so Benjamin could locate the Orb of the Emissary.
In this version, Ezri attempted to twice contact the Nile from the planet's surface to beam herself, Jake and Joseph aboard, due to exhaustion, but the runabout did not respond to her combadge. Later, after Benjamin located the Orb of the Emissary, Dax was successfully able to contact the Nile and requested the four of them to be beamed up.
Although no runabout was mentioned by name in the episode, the ship was visually identified on-screen as the USS Rio Grande.